RNA interference (RNAi) has recently emerged as a promising new avenue for treating a wide range of disease conditions. However, there are a few practical problems associated with the use of RNAi as an effective therapeutic method.
One potential problem is that the repression of a disease associated mRNA is often insufficient to treat the disease itself. For example, the Panc-1 and Mia-Paca mutant forms of K-Ras are associated with more than 95% of pancreatic cancers. However, repression of either mutant gene is insufficient for killing the cancer cell (Fleming et al., Molecular Cancer Research 3: 413, 2005). An alternative strategy might involve repression of normal mRNAs that cancer cells up-regulate for proliferation. However, much like chemotherapy, this may cause non-specific harms to healthy cells and tissues, thus necessitating the delivery of RNAi complexes at a lower potency that may give cancer cells an opportunity to evolve drug resistance.
Another example is the treatment of nuclear integrating viruses such as HIV. While RNA interference may be able to temporarily stop viral replication by repressing key viral mRNAs, the presence of pro-viral DNA in the nucleus of long lived latent cells means that viral mRNAs could reemerge to reinitiate replication once treatment stops.
In addition, RNA interference often has side effects associated with the non-specific repression of mRNAs with partial sequence homology to the intended target (“off-target effect”). This problem could occur when multiple mRNAs in the same cell all have 3′-UTR regions susceptible to miRNAs targeted at one particular mRNA. In this case, attempt to inhibit the expression of one specific target gene could lead to simultaneous expression knock-down of others unintended targets in both diseased and healthy cells. This problem could also occur when a disease mRNA target is a close homolog of a wild type, as in, for example, single nucleotide polymorphisms. In this case, healthy cells may have their mRNAs repressed by RNA interference intended to target mutant genes.
Yet another problem frequently associated with RNAi therapy is the recognition of double stranded RNA structures by cellular immunity. Proteins associated with cellular immunity, such as Toll Like Receptors (TLR), duplex RNA binding protein kinases, Rig1 and others, could lead to apoptosis, interferon production, inducement of inflammation and other side effects in the presence of long stretch of double-stranded RNAs.